This is a small tool that helps to draw the current genbank or refseq genome count through time, indicating the most common species and filtering down on specific groups if need be.
you can clone the git repository, go to its root and run:
python setup.py install
or
pip install .
This will install dependencies and the command line tool.
drawbank can be called with or without options. It will download the latest assembly summary, or use the one provided through the command line. By default it will display the number of genomes added each year.
To see the more usual 'cumulative count of genomes added each year", you can do it as such:
drawbank -c
draw something akin to this (it was drawn in early 2021 which is why 2020 and 2021 look alike), and display it in your browser.
You can filter down to any group of interest, for example looking only at plants:
drawbank -c -g plants
All options can be viewed using drawbank -h:
usage: drawbank [-h] [-m MOST_NUMEROUS_GROUP] [-c] [-s {genbank,refseq}] [-g GROUP] [-N] [--assembly ASSEMBLY] [--verbose] [--version]
Draws the current number of genomes in GenBank, with the given filters
optional arguments:
-h, --help show this help message and exit
Figure:
-m MOST_NUMEROUS_GROUP, --most_numerous_group MOST_NUMEROUS_GROUP
Indicate the n most numerous group (default: 5)
-c, --cumulative make a cumulative bar chart rather than have each year's addition (default: False)
Data source:
-s {genbank,refseq}, --section {genbank,refseq}
Section to download from (default: genbank)
-g GROUP, --group GROUP
comma separated list of groups to download from (any value among
all,archaea,bacteria,fungi,invertebrate,metagenomes,plant,protozoa,vertebrate_mammalian,viral,vertebrate_other,other) (default: all)
-N, --no_cache Do not cache downloaded files (nor use cached files). (default: False)
Misc options:
--assembly ASSEMBLY An assembly summary to use (if not provided, will download the latest one automatically) (default: None)
--verbose show the DEBUG log (default: False)
--version show program's version number and exit
They are all listed in the requirements.txt file.
- python>=3.6
- plotly>=4.0
- appdirs
- requests
- ete3>=3.0
- python-dateutil
- pandas